You ever played any modern JRPG? I'm 99% sure Pokemon is the ONLY RPG that still uses random encounters.

You don't need random encounter to get surprised of getting a rare Pokemon nor does do you need to it to reward patience. Hell just seeing it in the overworld alone is a surprise on its own, and if they don't want you to catch it easily it can run away instead of trying to attack you. I know in Persona 3 when you find a rare shadow it'll run away right when it sees you.